Background: The N-acetyltransferase 2 (NAT2) enzyme has been understudied in Nigerians including genotype-phenotype association studies. Objective: Study objective was NAT2 haplotype identification and genotype-phenotype investigations in HIV-positive and HIV-negative Nigerians. Method: Phenotypes included self-reported sulphonamide hypersensitivity survey, experimental and computational NAT2 phenotyping. NAT2 gene was amplified via polymerase chain reaction. Gene sequencing employed ABI 3730 and Haploview 4.2 for haplotype reconstruction. Genotypephenotype analyses used Chi square p-value and odds ratio with 95% confidence interval. Results: Self-reported sulphonamide hypersensitivity revealed prevalence of 3.1% and 12.4% in HIV-positive and HIV-negative Nigerians respectively. NAT2 genetic variants 191G>A, 282C>T, 341T>C, 481C>T, 590G>A, 803A>G and 857 G>A were not significantly different between both groups (OR 0.87 95%CI 0.54-1.38 P = 0.55). Nine haplotypes: NAT2*4, NAT2*12A, NAT2*13A, NAT2*5B, NAT2*6A, NAT2*7B, NAT2*5C, NAT2*14B and NAT2*14A had frequencies > 1% while NAT2*12B had 1.1% in HIV-positive and 0.4% in HIV-negative group. Overall, slow acetylator haplotypes made up 68%. NAT2*12 signature SNP (sSNP) was in high linkage