Background We investigated the association between chlamydia detection and stage in the menstrual cycle to investigate whether chlamydia detection was higher at different stages of the cycle.

Methods Electronic medical records for women attending Melbourne Sexual Health Centre March 2011 – 31^st December 2012, who were tested for chlamydia by nucleic acid amplification of high vaginal, cervical, or urinary samples, and who recorded a date of Last Normal Menstrual Period (LNMP) between 0–28 days were included in the analysis. Logistic regression was used to calculate OR (95% CI) for the association of chlamydia with menstrual cycle adjusted by demographics and behavioural variables.

Results During the study period, there were 10,017 consultations with positive diagnoses in 417 of those with a valid recorded LNMP. Detection rates were 3.8% (233/6816) in the follicular and 4.8% (184/3831) in the luteal phase of the menstrual cycle (OR 1.29 95% CI 1.1 – 1.6, p = 0.01). Detection was significantly associated with the luteal phase (adjusted odds ratio (aOR) 1.4 (95% CI 1.1–1.8) when adjusted for age, number of male partners, symptoms, inconsistent use of condoms, site of sample and sexual partners overseas/from overseas. Among women using hormonal contraception, there was no association with the luteal phase (aOR 1.3, 95% CI 0.9 – 1.8, p = 0.18; among women not using hormonal contraception, association with the luteal phase was significant (aOR 1.6, (95% CI 1.1 2.3, p = 0.007). The positive stored samples will undergo analysis to quantify bacterial load and determine if mean load differs across the cycle.

Conclusions Chlamydia detection rates are substantially and significantly higher in the luteal phase of the menstrual cycle. Hormonal and immune changes in the female reproductive tract may contribute to an increased burden of chlamydia infection in this phase, illustrated by the lack of association with the menstrual cycle in women using hormonal contraception.