Spatial abilities are known to be related to testosterone levels in men. Polymorphisms of genes related to androgen metabolism, however, have not been previously analyzed in association with spatial abilities. Our study analyzes genetic polymorphisms of androgen receptor (AR), aromatase (CYP19), and 5-alpha reductase (SRD5A2) in relation to mental rotation and spatial visualization in prepubertal intellectually gifted boys. DNA samples of 36 boys with an average age of 10.0 ± 0.7 years and an IQ higher than 130 were isolated from buccal cells in saliva. DNA was subsequently used for amplification by PCR. The CYP19 C1558-T polymorphism and SRD5A2 A49T polymorphism were determined by RFLP analysis, and the AR (CAG)n polymorphism was determined by fragment analysis. Salivary testosterone levels were measured with radioimmunoassay. Spatial abilities (mental rotation and spatial visualization) were assessed using standard psychometric tests. AR and CYP19 polymorphisms were not associated with spatial abilities. Heterozygotes in A49T polymorphisms (AT) of SRD5A2 had significantly better results in both mental rotation and spatial visualization tests compared to AA homozygotes. TT homozygotes were not found. The T allele of A49T polymorphism of the SRD5A2 was reported to have a 5-fold increased activity in comparison to the A allele. AT heterozygotes outscored AA homozygotes in tests of spatial performance. Since dihydrotestosterone – the product of 5-alpha reductase catalyzed reaction – has a higher affinity to AR, this might indicate a potential molecular mechanism for the influence of SRD5A2 polymorphism on spatial abilities in intellectually gifted prepubertal boys.