Abstract Background Polycystic ovary syndrome (PCOS) is a common endocrine disorder in women of fertile age and is associated with several burdensome comorbidities. We use Swedish longitudinal register data to identify and compare clusters of employment trajectories among working age women, in order to investigate how PCOS affects labor market attachment. Data and Methods A cohort of 157,356 women born in 1975-1977 were followed annually between the ages of 30 and 39. Labor market states were constructed by combining detailed data on various types of earned income. PCOS was identified through national inpatient and outpatient registers. Sociodemographic covariates (civil status, region of origin, highest attained education, number of children) were measured at the age of 29 years. Sequence analysis was used to identify clusters of typical labor market trajectories. Multinomial logistic regression was employed to assess the associations between being diagnosed with PCOS and belonging to the identified clusters. Results Women with PCOS spent less time in employment and were more dependent on sickness benefits during the follow-up time than those without PCOS. Five clusters of trajectories were identified: stable employment, education into employment, labor market exclusion, continuous unstable position, long-term sickness. Compared to being in stable employment cluster, women diagnosed with PCOS were 97% more likely to experience long-term sickness (RRR (relative risk ratio): 1.97 [CI: 1.90-2.05]), and had 11% higher risk of belonging to education into employment (RRR: 1.11 [CI: 1.07-1.15]) and a 4% higher risk (RRR: 1.04 [CI: 1.00-1.09]) of experiencing labor market exclusion. The magnitude of the association increased for education into employment and labor market exclusion after adjusting for covariates. Conclusions PCOS can lead to disadvantaged labor market outcomes and better strategies are needed in order to prevent economic exclusion among women diagnosed with the condition. Key messages • PCOS leads to disadvantaged labor market outcomes. • Women with PCOS may experience economic exclusion.