Aim: Acute lower respiratory infections (ALRIs) are the most common reason for hospitalisation of young children in the Northern Territory of Australia. International studies have linked vitamin D deficiency with increased risk of ALRI in paediatric populations, but this has not been explored in tropical regions such as the Top End of the Northern Territory. The aim of this study is to determine the prevalence of vitamin D insufficiency among children hospitalised with ALRI in the Northern Territory. Methods: Vitamin D serum metabolite (25OHD3) levels were retrospectively measured using liquid chromatography–mass spectrometry in 74 children (64% male; 57% Indigenous) aged less than 3 years admitted to Royal Darwin Hospital in the Northern Territory of Australia between May 2008 and May 2010. Results: There were 44 (59%) ALRI-classified hospitalisations and 30 (41%) non-ALRI-classified hospitalisations. The most common ALRI diagnoses were bronchiolitis (n = 22, 30%) and pneumonia (n = 21, 28%), whereas the most common non-ALRI diagnosis was gastroenteritis (n = 20, 27%). Overall, 24/74 (32%) children had 25OHD3 levels <75 nmol/L (insufficiency). For children hospitalised with ALRI, 23% (10/44) had vitamin D insufficiency compared with 47% (14/30) among children hospitalised for other reasons (odds ratio 0.34, 95% confidence interval 0.11–1.03; P = 0.043). Twelve of the 20 (60%) children hospitalised for gastroenteritis had vitamin D insufficiency. Conclusions: Vitamin D insufficiency was observed in almost one-third of these hospitalised children. Children hospitalised with an ALRI were less likely to have vitamin D insufficiency compared with children hospitalised for other conditions (predominantly gastroenteritis).