The problems encountered during scuba diving may be a contributing factor in an episode of decompression illness (DCI). Evidence exists that there may be a relationship between the position in the menstrual cycle and the occurrence of DCI. We examined, by prospective observation in female recreational scuba divers, any interaction between reported problems during diving (RPDD) and the position in the menstrual cycle. A total of 533 women, aged between 14 and 57 years, returned diaries for >6 months, with 61% returning diaries for 3 consecutive years. A total of 34,625 dives were reported within 11,461 menstrual cycles between 21 and 40 days in length, with 65% of women reporting at least one RPDD. Logistic regression showed a significant non-linear relationship between the position in the menstrual cycle and RPDD (p = 0.004). RPDD were not evenly distributed over the menstrual cycle; the rate per 1,000 dives varied from 39.2 at start of the cycle to 19.7 during week 3, and 31.9 in week 4. We concluded these field data suggest a possible correlation between the incidence of RPDD and the position in which they occurred in the menstrual cycle.