The pathological sequelae of untreated homocystinuria due to cystathionine beta-synthase deficiency include ectopia lentis, osteoporosis, thromboembolic events and mental retardation. They occur at a significantly higher rate with poorer mental capabilities (mean IQ = 57) in the untreated pyridoxine-nonresponsive individuals. The mental capabilities of 23 pyridoxine-nonresponsive individuals with 339 patient-years of treatment were assessed using age-appropriate psychometric tests and were compared to those of 10 unaffected siblings (controls). Of the 23 individuals, 19 were diagnosed through newborn screening with early treatment, two were late-detected and two were untreated at the time of assessment. Thirteen of the newborn, screened group who were compliant with treatment had no complications, while the remaining 6, who had poor compliance, developed complications. Good compliance was defined by a lifetime plasma free homocystine median < 11 micromol/L. The newborn screened, good compliance group (n = 13) with a mean age of 14.4 years (range 4.4-24.9) had mean full-scale IQ (FIQ) of 105.8 (range 84-120), while the poorly compliant group (n = 6) with a mean age of 19.9 years (range 13.8-25.5) had a mean FIQ of 80.8 (range 40-103). The control group (n = 10) with mean age of 19.4 years (range 9.7-32.9) years had a mean FIQ of 102 (range 76-116). The two late-detected patients aged 18.9 and 18.8 years had FIQ of 80 and 102, while the two untreated patients aged 22.4 and 11.7 years had FIQ of 52 and 53, respectively. There was no statistical evidence of significant differences between the compliant, early-treated individuals and their unaffected siblings (controls) except for the FIQ, which was significantly higher than that of the unaffected siblings (p = 0.0397). These data, despite the relatively small numbers, suggest that early treatment with good biochemical control (lifetime plasma free homocystine median < 11 micromol/L) seems to prevent mental retardation.