In Spain, anti-pneumococcal vaccination is recommended for all children under 2 years old, high-risk groups and adults ≥65 years old. However, it is not funded in most autonomous communities. This study aims to compare pneumococcal disease hospitalisation rates between Period 1 (2007-2009), when 7-valent (PCV7) vaccine was available, and Period 2 (2011-2013), after the change to 13-valent (PCV13) vaccine in Spain. Data on hospitalisations were obtained from the National Registry of Hospitalisations. We calculated hospitalisation rates (HRs) and hospitalisation rate ratios (HRRs) among periods by age group and autonomous community, for all and by clinical presentation. From 138,361 patients hospitalised, 83,528 (60.4 %) were males. The median age was 73.8 years. The most common clinical presentation was pneumonia (133,204 hospitalisations; 96.3 %), followed by septicaemia (7053 hospitalisations; 5.1 %) and meningitis (3182 hospitalisations; 2.3 %). In Period 2, hospitalisations among children <5 years old decreased for pneumonia [HRR: 0.37; 95 % confidence interval (95 % CI): 0.35 to 0.39] and meningitis (HRR: 0.53; 95 % CI: 0.44 to 0.65). For adults ≥65 years old, pneumonia (HRR: 0.49; 95 % CI: 0.49 to 0.50) and peritonitis (HRR: 0.34; 95 % CI: 0.19 to 0.63) hospitalisations decreased and septicaemia hospitalisations (HRR: 1.27; 95 % CI: 1.18 to 1.36) increased. Significant changes in HRs for pneumococcal disease were observed even without an integrated and continuous vaccination programme after the introduction of PCV13, especially in children <5 years old and for pneumonia. The impact of the PCV13 adult vaccination new recommendations on the septicaemia increase reported should be evaluated in the future.