Factor XIII (FXIII) has an important role in the control of bleeding through fibrin cross-linking; however, its effect within the menstrual cycle is not fully understood. The aim of this study was to examine changes in FXIII activity during the normal menstrual cycle and correlate FXIII activity with menstrual blood loss. A total of 32 healthy normal women of reproductive age were recruited. Menstrual blood loss was measured using the pictorial blood-assessment chart (PBAC). A bleeding score questionnaire was also completed. Blood samples were taken during the menstrual, proliferative, periovulatory, secretory and premenstrual phase for assessment of FXIII level. The mean ± SD FXIII level was lowest during menstrual and periovulatory phases (114 ± 23 and 114 ± 21 IU/dl, respectively). Mean FXIII level during the secretory and premenstrual phases were higher than the menstrual phase (P = 0.036). Mean secretory phase FXIII was also significantly higher compared with the periovulatory phase (P = 0.02). There was no significant correlation between FXIII level during the menstrual phase and age (P = 0.53) or PBAC score (P = 0.53). There were no significant differences in FXIII level during the menstrual phase between women with PBAC scores of at least 100 (n = 14; mean 116 IU/dl) and women with PBAC scores less than 100 (n = 18; mean 113 IU/dl). There was no correlation between FXIII level and bleeding score. FXIII activity was lower during menstrual and periovulatory phases of the cycle. However, the small difference between mean values (8 IU/dl) would be unlikely to have a significant impact on diagnosis of FXIII deficiency and clinical management.