An encoder/decoder system for 3D volumetric medical data is proposed. The system allows fast access to any 2D image by decoding only the relevant information from each subband image and thus provides minimum decoding time. This will be of immense use for the medical community because most of the computerised tomography, magnetic resonance imaging and positron emission tomography modalities produce volumetric data. As a fully fledged 3D wavelet transform is used for compression, the advantage of good compression ratio is preserved. Preprocessing is carried out prior to wavelet transform, to enable easier identification of coefficients from each subband image. Inclusion of special characters in the bit stream (markers) facilitates access to corresponding information from the encoded data. Experiments are carried out by performing Daub4 filter along x (row) and y (column) directions and Haar filter along the z (slice) direction to account for the difference between interslice and intraslice resolution. The performance of the system has been evaluated on four sets of volumetric data and the results are compared to other 3D encoding/2D decoding schemes. Results show that for slice spacing of 3–10 mm, there is substantial improvement in decoding time. The speedup is found to be 2.