BACKGROUND: Following independence from the Soviet Union in 1991, Estonia introduced a national insurance system, consolidated the number of health care providers, and introduced family medicine centred primary health care (PHC) to strengthen the health system. METHODS: Using routinely collected health billing records for 2005-2012, we examine health system utilisation for seven ambulatory care sensitive conditions (ACSCs) (asthma, chronic obstructive pulmonary disease [COPD], depression, Type 2 diabetes, heart failure, hypertension, and ischemic heart disease [IHD]), and by patient characteristics (gender, age, and number of co-morbidities). The data set contained 552 822 individuals. We use patient level data to test the significance of trends, and employ multivariate regression analysis to evaluate the probability of inpatient admission while controlling for patient characteristics, health system supply-side variables, and PHC use. FINDINGS: Over the study period, utilisation of PHC increased, whilst inpatient admissions fell. Service mix in PHC changed with increases in phone, email, nurse, and follow-up (vs initial) consultations. Healthcare utilisation for diabetes, depression, IHD and hypertension shifted to PHC, whilst for COPD, heart failure and asthma utilisation in outpatient and inpatient settings increased. Multivariate regression indicates higher probability of inpatient admission for males, older patient and especially those with multimorbidity, but protective effect for PHC, with significantly lower hospital admission for those utilising PHC services. INTERPRETATION: Our findings suggest health system reforms in Estonia have influenced the shift of ACSCs from secondary to primary care, with PHC having a protective effect in reducing hospital admissions.