Objectives. We studied a group of female renal transplant patients and patients receiving dialysis to determine the natural history of human papillomavirus (HPV) type 16 DNA infection in the two groups and its effect on lower genital tract intraepithelial neoplasia development and progression. Materials and Methods. Female renal transplant and dialysis patients were recruited from the renal unit of the hospital. Follow-up was every 6 months, and all women were seen at least twice. Assessment was obtained by cytology, colposcopy, directed biopsy, and HPV 16 DNA semiquantitative analysis by polymerase chain reaction. The oligonucleotide primers were designed to amplify a 233–base pair region of the HPV 16 E6 and E7 genes (nucleotides 491–714), with confirmation of the amplified product performed by Southern blotting and probing with an oligonucleotide probe specific to an internal portion of the ampli-con. Results. The 28 transplant patients and 14 dialysis patients were followed up for an overall mean of 14.6 months (range, 5–24 months; median, 18 months). Only one dialysis patient was positive for the HPV 16 genome, and this was in low copy numbers. The HPV status changed in some patients throughout the study period; however, no one who had medium-high or high copy numbers at enrollment became HPV 16 DNA–negative. From study entry, HPV 16 DNA positivity was associated with progression of preexisting intraepithelial disease and new disease development, although the association was not statistically significant by either log-rank or Cox’s proportional hazard model ( p = .76 and .77, respectively). Neither coexisting cervical intraepithelial neoplasia (CIN) nor type of renal disease nor the therapeutic regimen used at study entry appeared to influence disease development and progression ( p = .42 and .7, respectively). The only factor that influenced development and progression of CIN from study entry was the length of time from transplantation ( p = .01). Time from transplantation did appear to influence HPV 16 DNA positivity ( p = .04), but the combined influence did not hold up to scrutiny in a multivariate analysis using Cox’s proportional model ( p = .34), suggesting that HPV 16 positivity was a surrogate marker for time from transplantation. Conclusions. HPV 16 DNA positivity alone is an inadequate explanation for the development and progression of lower genital tract intraepithelial disease in women with renal transplant. The length of time from transplantation is an important factor, but the exact association between duration of immune suppression and CIN has yet to be clarified.