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Objectives The objective of this study was to evaluate the association between estimated human papillomavirus ( HPV) viral load and abnormal cytology on anal samples. Methods Anal cytological samples of 42 HIV-positive patients were analysed by conventional cytology and Hybrid Capture II. Results On cytology, 30.95% (13 of 42) anal samples were positive for cytological abnormalities, 47.61% (20 of 42) were negative and 21.42% (nine of 42) were unsatisfactory. High-risk HPV infection was more frequent in anal samples with cytological abnormalities than in negative samples ( P = 0.0002, Fisher's exact test), it was detected in all samples with cytological abnormalities and in 35% (seven of 20) of the negative samples. On samples with cytological abnormalities, the median of the relative light unit/cutoff ( RLU/ CO) value (viral load estimate) was 10.39 (1.02-572.6) and in negative samples it was 0.51 (0.26-51.70). The median of the RLU/ CO value was higher in samples with cytological abnormalities when compared with the median in negative samples ( P = 0.0001, Mann-Whitney U-test) and only samples with cytological abnormalities showed RLU/ CO values > 100. Conclusions The estimated high-risk HPV viral load is significantly higher in samples with cytological abnormalities than in negative anal samples and may be useful as an adjunct to anal cytology for triage of patients to high-resolution anoscopy and biopsy. [ABSTRACT FROM AUTHOR]