Heat exchangers are key components of energy conversion systems, including HVAC&R equipment. The compact microchannel design of a heat exchanger (MCHX) allows for significant reduction of its volume, weight, and raw material, in comparison to conventional fin-and-tube heat exchangers in HVAC&R systems. The current generation of microchannel evaporators along with advantages, such as high heat transfer rate and reduced refrigerant charge, encounters important problems related to flow maldistribution and instabilities in parallel-channels flow. The thermal and hydrodynamic performance of a microchannel evaporator can drastically decrease, due to the presence of instabilities, and maintaining a set point for operational parameters can become challenging. Microchannels are characterized by a large ratio of surface area to fluid volume, and rapid growth of bubbles in a confined space causes flow parameter oscillations. Fluctuations in pressure, pressure drop, temperature and mass flux can be triggered in the individual channels (ports) and they can affect neighboring channels. For instance, flow oscillations in parallel channels can lead to premature initiation of dryout that reduces the overall heat transfer. This research is motivated by the challenge of predicting flow boiling instabilities in parallel channels, since understanding the nature of these instabilities and their relationship to the operational parameters can be advantageous for the engineering community. Analysis of the pressure drop behavior in parallel non-uniformly heated microchannels is chosen as the primary method to explore instabilities. The possible nonuniformity of heat flux from channel to channel was studied by solving the conjugate, three-dimensional, transient heat transfer problem of louvered fins bounded with multiport aluminum plates using commercial software (ANSYS FLUENT). While the fin geometry was kept constant in all simulations, two different multiport plate configurations (11 round ports, D=1.2 mm; and 22 square ports, 0.54x0.54 mm) were analyzed at two air face velocities, 1m/s (Re_Lp = 82) and 5m/s (Re_Lp = 410), and two temperature differences, 10K and 20K, between the incoming air and the inside walls of the channels that have constant temperature of 10oC. Air flow was louver directed in both cases, while the large scale vortex shedding from the plate, in addition to the unstable wake of the exit louver, was observed at Re_Lp = 410. The magnitude of the heat flux difference between ΔT=10K and ΔT=20K cases was two times. The results show that the first channel, facing the flow, has the highest heat flux in all cases. The variation of the channel-to-channel heat flux downstream from the leading edge was dependent on the incoming flow velocity and air flow morphology. The overall heat flux difference between the leading channel and the trailing one was 73% at the incoming air velocity of 5 m/s, while this difference was almost 96% at lower velocity of 1 m/s. It might be concluded that a higher air velocity (mass flow rate) corresponds to a lower temperature drop for the air stream, and less variation in the temperature driving potential (port to port) causes less heat flux variation. Overall, the results of numerical simulations prove the presence of heat flux variation between neighboring channels; therefore, the effects of channel-to-channel heat flux variations on flow maldistribution and flow boiling instabilities between neighboring microchannels were considered. The region of significant flow boiling instabilities in multiple, nonuniformly heated channels bounded by constant pressure drop is predicted by modeling the pressure drop behavior in each individual channel using the internal characteristic or ΔPi-Gi curve. Combination of parallel channels ΔPi-Gi curves and definition of possible flow rate solutions at a given constant pressure drop across all channels can be used to demarcate regions of possible instabilities. In order to accomplish this, theoretical modeling of a single channel ΔP-G curve is undertaken in this research. Two-phase pressure drop was modeled based on semi-empirical correlations of the frictional two-phase pressure drop by Kim & Mudawar (2014), and the void fraction model by Xu & Fang (2014). A single channel characteristic curve model was experimentally validated for two channel sizes 2 mm and 1 mm using refrigerant R245fa at T_sat=24.5oC. The theoretical model consistently predicted the trends in the data very well, and it predicted pressure drop within 19.3% for the 2 mm tube and within 32.5% for the 1 mm tube. Furthermore, the effect of fluid properties, operational parameters, and geometrical parameters of a channel on a single channel ΔP-G curve behavior is theoretically analyzed. The span of the negative slope region (where instability is manifested) depends on with saturation conditions, inlet subcooling, heat flux, channel size and length, and fluid type. The negative slope region decreases with decreasing heat flux, liquid and vapor densities ratio, and as channel becomes shorter and smaller due to the reduced vapor generation. The negative slope region also decreases with increasing saturation pressure, specific heat and degree of subcooling. Multiple channel instabilities are analyzed by combining individual ΔPi-Gi curves of 2-6 unevenly heated microchannels and seeking flow rate solutions at a given constant pressure drop across multiple channels. Theoretical results show that for a given total flow rate the flow may split among parallel pipes in various ways satisfying the equal pressure drop condition in all channels; there exist a range of the incoming flow rates where maldistribution is the only possible solution. Furthermore, linear stability analysis was performed to differentiate between stable and unstable solutions. The analysis enabled the demarcation of unstable regions on the total ΔP-G curve. Therefore, it is possible to anticipate unstable regions if the inlet flow rate, number of channels, and operational parameters are known. In conclusion, this research is focused on the study of flow boiling in parallel microchannels subjected to uneven heat flux. Understanding the single channel pressure drop versus flow rate (ΔP-G) characteristic curve, and understanding the interactions between channels leads to the development of a map that demarks unstable regions. This map can provide guidance to engineers in choosing operational conditions and developing compact evaporators. Therefore, the results of this work have significant impact on understanding flow boiling behavior in multiple microchannels that could lead to practical applications.