BACKGROUND: Current studies comparing musculoskeletal pain levels between the genders focus on a single point in time rather than measuring change over time. The purpose of this study is to compare pain levels between males and females before and after treatment. METHODS: Eleven different patient cohorts (3,900 patients) included in two prospective outcome databases collected pain data at baseline and 1 month after treatment. Treatments were either imaging-guided therapeutic injections or chiropractic therapy. The Mann-Whitney U test was used to calculate differences in numerical rating scale (NRS) median scores between the genders for both time points in all 11 cohorts. RESULTS: Females reported significantly higher baseline pain scores at 4 of the 11 sites evaluated (glenohumeral (p = 0.015), subacromial (p = 0.002), knee (p = 0.023) injections sites and chiropractic low back pain (LBP) patients (p = 0.041)). However, at 1 month after treatment there were no significant gender differences in pain scores at any of the extremity sites. Only the chiropractic LBP patients continued to show higher pain levels in females at 1 month. CONCLUSIONS: In these 11 musculoskeletal sites evaluated before and after treatment, only 3 extremity sites and the chiropractic LBP patients showed significantly higher baseline pain levels in females. At 1 month after treatment only the LBP patients had significant gender differences in pain levels. Gender evaluation of change in pain over time is likely to be more clinically important than an isolated pain measurement for certain anatomical sites.