Eighty morphophysiological traits were studied in 55 males with a morphologically identical heterochromatin subtotal deletion of Y chromosome and in 55 males with a normal Y chromosome. No significant differences were found between these groups in mean values of most traits except some hematologic parameters. Using the pattern recognition algorithm a combination of 20 traits which differentiated the groups under comparison with the recognition errors 4.6% was extracted. The recognition system consisted the informative traits including electrocardiographic parameters (25% of the traits), some anthropological and hematologic traits and subjects' age. The results suggest that the Y chromosome heterochromatin appears to have a modifying effect on the phenotypic relationship between morphophysiological traits during human ontogenesis.