While nutritional, microbiological and immunological factors have been implicated in childhood diarrhoea in many countries, there is limited aetiological information in Morogoro Region of Tanzania. A case-control study was conducted to establish whether diarrhoea in 6-60 months old children admitted at a Regional Hospital in Morogoro, was attributable to enteric bacteria and/or parasites and the contribution of under-nutrition, as measured by weight-for-age below -2 SD. From January to September 2011, children admitted at the Hospital with (cases) and without diarrhoea (controls), were obtained by convenience sampling. Children’s stool, weights, ages and information on socioeconomic, feeding, water and sanitation factors were obtained. Stool samples were analysed for Escherichia coli O157 , Shigella dysentriae, Campylobacter jejuni, Salmonella species and enteric parasites. Logistic regression was used to identify their association with diarrhoea occurrence; and survival analysis used to assess associated risk, using associated hazard ratios (HR). Commonest bacteria isolated were Salmonella , more from controls, 45 (29.6%), than cases, 25 (16.6%); S. dysentriae and C. jejuni were only isolated from cases, while E coli O157 was not found. Enteric parasites were least prevalent; 4 (2.6%) for cases and 2 (1.3%) for controls. Although under-weight children had 38% increased risk of having diarrhoea than normal ones, this was not significant (HR = 0.98, p =0.928). Other factors found to significantly ( p <0.05) influence diarrhoea occurrence included age when breastfeeding stopped, food(s) given, feeding utensils and the child´s toilet. In conclusion, childhood diarrhoea occurrence should warrant microbiological testing, for timely, appropriate treatment and prevention of transmission to others. Prevention and control measures for diarrhoea in children in Morogoro should include adequate breastfeeding, proper disposal of children’s faeces and feeding children using cups rather than bottles. The increased occurrence of diarrhoea among malnourished children, particularly upon breast milk withdrawal, gives food and nutrition prominence among control measures.