Pneumonia and diarrhea are leading causes of child deaths in Malawi. Guidelines to manage childhood illnesses in resource-poor settings exist, but studies have reported low health-care worker (HCW) adherence to guidelines. We conducted a health facility survey from January to March 2015 to assess HCW management of pneumonia and diarrhea in children < 5 years of age in southern Malawi, and to determine factors associated with case management quality. Descriptive statistics and multivariable logistic regression models examined patient, HCW, and health facility factors associated with recommended pneumonia and diarrhea management, using Malawi's national guidelines as the gold standard. Of 694 surveyed children 2-59 months of age at 95 health facilities, 132 (19.0%) met survey criteria for pneumonia; HCWs gave recommended antibiotic treatment to 90 (68.2%). Of 723 children < 5 years of age, 222 (30.7%) had uncomplicated diarrhea; HCWs provided recommended treatment to 94 (42.3%). In multivariable analyses, caregivers' spontaneous report of children's symptoms was associated with recommended treatment of both pneumonia (odds ratio [OR]: 2.8, 95% confidence interval [CI]: 1.2-6.8, = 0.023) and diarrhea (OR: 24.2, 95% CI: 6.0-97.0, < 0001). Malaria diagnosis was negatively associated with recommended treatment (OR for pneumonia: 0.5, 95% CI: 0.2-1.0, = 0.046; OR for diarrhea: 0.3, 95% CI: 0.1-0.6, = 0.003). To improve quality of care, children should be assessed systematically, even when malaria is suspected. Renewed efforts to invigorate such a systematic approach, including HCW training, regular follow-up supervision, and monitoring HCW performance, are needed in Malawi.

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