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Objective: To determine the accuracy of high‐risk human papillomavirus (HPV) DNA samples on filter paper in comparison to specimen transport medium (STM). Methods: This was a cross‐sectional diagnostic study of 42 consecutive women who were prospectively recruited. Each had self‐collected vaginal samples on filter paper, physician‐collected cervical samples on filter paper, and physician‐collected cervical samples in STM. HPV DNA testing was performed with a Hybrid Capture 2 system (Qiagen). Sensitivity, specificity, negative predictive value (NPV), positive predictive value (PPV), and agreement of filter paper methods with the standard procedure were calculated. Results: The overall prevalence of HPV in STM was 67.5%. Detection of HPV DNA in the physician‐collected cervical samples on filter paper had a sensitivity of 77.8%, a specificity of 100%, a PPV of 100%, and an NPV of 68.4%. The patient's self‐sampling on filter paper had a sensitivity of 66.7%, a specificity of 100%, a PPV of 100%, and an NPV of 59.1%. The agreement between STM method and physician‐collected sample on filter paper was substantial, (κ = 0.695, P < 0.001), while the agreement between STM and self‐collected samples on filter paper was moderate (κ = 0.565, P < 0.001). Most patients reported that self‐collection was acceptable (100%), painless (95%), and not embarrassing (95%). Conclusion: Filter paper, with dried self‐collected vaginal samples, can be used to detect high‐risk HPV with acceptable accuracy. Synopsis: Self‐collected vaginal samples on filter paper, to detect high‐risk human papillomavirus, is better for women, easier to transport to central laboratories, and has acceptable accuracy. [ABSTRACT FROM AUTHOR]