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In low- and middle-income countries, undernutrition often co-exists with intestinal parasites, especially Soil Transmitted Helminth (STH) infections in children. The collective impact of both conditions result in undernutrition and can exacerbate the general poor health status of children. A cross-sectional survey of 422 mother-child (12-59 months old) pairs from 14 villages in the District of Ndelele, East Region of Cameroon, was carried out to assess the magnitude and correlates of undernutrition and intestinal parasites. Socio-demographic data were collected from mothers and anthropometric data were collected from children. Parasitological assessment was performed using a combination of direct microscopy flotation, sedimentation and centrifugation techniques. Correlates of undernutrition and intestinal parasites were identified using multinomial logistic regression at individual and household levels. 83.77% of the children assessed for undernutrition were undernourished and 66.82% were positive for one or more intestinal parasites. It was not uncommon for the study participants to be concurrently infected with two or more intestinal parasites. The most common intestinal parasitic infections detected in the study were A. lumbricoides, E. histolytica/dispar and Hookworm infection. Multinomial logistic regression using Nutritional status as outcome showed that, children who were not exclusively breastfed were 106% (RR = 2.06; C.I = 1.12-3.80) more likely to be underweight compared to those who were exclusively breastfed. The household size of 4 to 6 persons also significantly impacted wasting (p-value = 0.007) at 7% (RR = 1.07, C.I = 0.49-2.32). Analysis by a logistic regression model with STH infection as outcome revealed that, Fingernail cleanness (p-value = 0.044; AOR = 1.75; CI = 1.09-2.78) and household size (p-value = 0.038; AOR = 0.55; CI = 0.32-0.92) were positively associated with intestinal parasite infection at the 5% significant level. This study reveals that intestinal helminthic parasitic infections (STH) and undernutrition are serious health problems in children below five in the study area. To address this dire situation, concerted efforts are needed to improve sanitation, hygiene education access, community deworming programs, and improve diets. The authors thank the study participants, quarter heads, chiefs, data collectors and all staff of both the Ngotto and Banga health centers. We would also like to thank the University of Buea for support in materials and postgraduate funds. We are equally grateful to the Molecular and Cell Biology laboratory of the University of Buea for their support in the accomplishment of this study. We thank the field staff and data collectors for taking their precious time to collect the data and most especially our field coordinator Mr Caleb Yengo and our data analyst Ms Rahmah Mahdiyatur.

Additional file 1. Distribution of sampled water bodies within the study sites in Akonolinga health district.

Additional file 1. Although not significant GMPD decreased with an increase in age in the high lands as well as the higher values observed in males than females in the low (465) and high lands (385). However, the GMPD/ µL of blood in males (465) and females (434) was significantly higher (P < 0.001) in the lowland when compared with the other altitudinal sites.

Additional file 2. Distribution of MU-positivity per sampled locality and sample type.