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To explore the reproductive endocrine feature and conception outcome of women with unknown etiological long menstrual cycle (LMC) (36–45 days) with long follicular phase. In the cohort study, we included 80 women with unknown etiological long menstrual cycle of biphasic basal body temperature (BBT) lasting for 36–45 days and 87 controls with normal cycle of biphasic BBT into LMC group and NMC group, respectively. Serum hormone levels, fasting glucose, and insulin of participants were tested, and ovulation was observed by ultrasound. The conception outcome was followed up within 12 menstrual cycles. In the LMC group, the rate of abnormality of HOMA-insulin resistance index (40.0% vs. 20.7%,  p  &lt; .01), luteal phase defect (30.9% vs. 13.8%,  p  &lt; .05) and abnormality of FSH/LH ratio (15.6% vs. 5.7%,  p  &lt; .05) were all significantly higher, but the serum estradiol level on the day before ovulation (261.10 pg/mL vs. 320.26 pg/mL,  p  &lt; .01) was lower. The rate of poor ovulation quality (31.3% vs.15.4%,  p  &lt; .05) in the LMC group was significantly higher than the NMC group. In the LMC group, the natural conception rate within 12 menstrual cycles was lower (41.9% vs. 66.2%,  p  &lt; .01), whereas the spontaneous abortion rate in early pregnancy (29.0% vs. 9.8%,  p  &lt; .05) and the conversion rate (21.6% vs. 5.2%,  p  &lt; .01) to anovulation within 12 cycles were significantly higher. Women with unknown etiological menstrual cycle (36–45 days) with long follicular phase have greater endocrine abnormality and higher risk of spontaneous abortion, infertility, and conversion to anovulation. Moderate early intervention may be advisable for these women, especially those who wish to get pregnant.

The reproductive endocrine feature and conception outcome of women with unknown etiological menstrual cycle (36–45 days) with long follicular phase