Although the Kenyan government has made efforts to invest in maternal health over the past 15 years, there is no evidence of decline in maternal mortality. To provide necessary evidence to inform maternal health care provision, we conducted a nationally representative study to describe the incidence and causes of maternal near-miss (MNM), and the quality of obstetric care in referral hospitals in Kenya. We collected data from 54 referral hospitals in 27 counties. Individuals admitted with potentially life-threatening conditions (using World Health Organization criteria) in pregnancy, childbirth or puerperium over a three month study period were eligible for inclusion in our study. All cases of severe maternal outcome (SMO, MNM cases and deaths) were prospectively identified, and after consent, included in the study. The national annual incidence of MNM was 7.2 per 1,000 live births and the intra-hospital maternal mortality ratio was 36.2 per 100,000 live births. The major causes of SMOs were postpartum haemorrhage and severe pre-eclampsia/eclampsia. However, only 77% of women with severe preeclampsia/eclampsia received magnesium sulphate and 67% with antepartum haemorrhage who needed blood received it. To reduce the burden of SMOs in Kenya, there is need for timely management of complications and improved access to essential emergency obstetric care interventions.