Finding microRNA targets in the coding region is difficult due to the overwhelming signal encoding the amino acid sequence. Here, we introduce an algorithm (called PACCMIT-CDS) that finds potential microRNA targets within coding sequences by searching for conserved motifs that are complementary to the microRNA seed region and also overrepresented in comparison with a background model preserving both codon usage and amino acid sequence. Precision and sensitivity of PACCMIT-CDS are evaluated using PAR-CLIP and proteomics data sets. Thanks to the properly constructed background, the new algorithm achieves a lower rate of false positives and better ranking of predictions than do currently available algorithms, which were designed to find microRNA targets within 3′ UTRs.