Official statistics routinely underestimate mortality from specific microorganisms and deaths are assigned to non-specific syndromes. Here we estimate mortality attributed to specific pathogens by modelling non-specific infant deaths from laboratory reports and codes on death certificates for these pathogens, 1993–2000 in England and Wales using a generalized linear model. In total, 22·4–59·8% of non-specific deaths in infants (25–66 deaths a year) are attributable to specific pathogens. Yearly deaths from Bordetella pertussis in neonates are 6·8 [95% confidence interval (CI) 1·5–11·9]. In post-neonates 9·4 (95% CI 2·3–16·6) deaths a year are attributable to Neisseria meningitidis, 7·3 (95% CI 2·4–12·3) to Streptococcus pneumoniae, from 2·8 (95% CI 0·8–4·9) to 15·1 (95% CI 9·4–20·9) to respiratory syncytial virus (RSV) and 3 (95% CI 0·3–5·9) to parainfluenza type 2. Our results suggest there is substantial hidden mortality for a number of pathogens in infants. A considerable proportion of deaths classified to infectious syndromes are non-infectious, suggesting low specificity of death certification. Laboratory reports were the more reliable source, reinforcing the asset of strong surveillance systems.