To determine whether NAT2 genotyping could be used interchangeably with caffeine phenotyping in assessing N-acetyltransferase activity in epidemiological studies, sources of interindividual variability in N-acetyltransferase activity were assessed among 90 subjects of various ethnic backgrounds in Hawaii. Forty-three subjects were patients with in situ colorectal cancer treated by polypectomy, and 47 were healthy population controls. Subjects were administered a lifestyle questionnaire and were evaluated for N-acetyltransferase activity by caffeine phenotyping. NAT2 genotype was also assessed by PCR amplification of peripheral leukocyte DNA for the M1, M2, and M3 variant alleles. Fifty-four % of the overall variation in acetylation activity was explained by the three genotype categories (homozygous variant, heterozygous, and homozygous wild-type). This proportion was reduced to 42% when genotype was modeled using only two categories ("slow" being homozygous variant; "rapid" being all others). Use of gout medications (probenecid or allopurinol), consumption of heavily browned fish, and P450IA2 activity (also measured by caffeine phenotyping), together explained another 11% of the variance. No association was found between acetylation activity and sex; race; age; education; smoking; physical activity; weight; consumption of coffee, alcohol, red meat, processed meat, and cruciferous vegetables; or use of menopausal estrogens, after taking genotype into account. Results were similar for colorectal cancer patients and controls. Considerable variation in acetylation activity was observed within the homozygous wild-type group. This study suggests that the use of genotyping, instead of phenotyping, to assess the association of acetylation with cancer risk is unlikely to introduce major misclassification or bias, especially when the three genotype categories are modeled and the sample size is large. However, when the rapid acetylation phenotype is the at-risk group (e.g., when studying colon career), phenotyping appears judicious given the variability in acetylation activity within this group.