We examined changes in sexual behavior and sexually transmitted infection (STI) prevalence among 183 men who have sex with men (MSM) initiating pre-exposure prophylaxis (PrEP) at an STD Clinic in Seattle, WA. We used generalized estimating equations to measure changes in sexual behavior during PrEP use, and linked PrEP patient data with STI surveillance data to compare the prevalence of chlamydia, gonorrhea, and early syphilis in the periods prior to and during PrEP use. Reporting never using condoms in the prior 30 days increased (adjusted relative risk = 1.46; 95% confidence interval 1.13, 1.88) at 12 months after PrEP initiation compared to the initial PrEP visit. Reporting unknown status partners in the prior 30 days decreased at 12 months compared to the initial PrEP visit, but there was no change in number of sexual partners or reporting HIV-positive or HIV-negative partners. The percentage of patients diagnosed with any STI while using PrEP (49.2%) was higher than the percentage diagnosed in the 12 months prior to PrEP use (35.0%), likely driven in part by increased STI screening during PrEP use. Among MSM on PrEP, we observed decreases in condom use, and a higher prevalence of STIs during PrEP use compared to prior to PrEP initiation.