Progressing economic development in Southeast Asia has increased regional demand for goat meat, leading to expanding production by smallholders and recently, development of commercial farms. In Laos, an emerging export market for goats into Vietnam has led to increased goat numbers, with potential increases in risk of disease, particularly endoparasitism. A cross-sectional survey investigated the prevalence of gastrointestinal parasites in indigenous Kambing-Katjang goats on smallholder farms (n = 389) in 8 villages where no anthelmintic treatments were in use, providing comparisons with a case study of imported Boer crossbred goats (n = 45) on a commercial farm where intensive anthelmintic treatments were required to manage mortalities attributable to Haemonchosis. Clinical examinations, collection of faecal samples, and pathological examination on the commercial farm, accompanied collection of information on animal gender, age and body weight, with data analyses performed in Genstat. Faecal samples contained eggs of multiple endoparasitic species, with Strongyles spp. and coccidian oocysts of Eimeria spp. most prevalent. Significant associations between the presence of endoparasites and the farm type (smallholder versus commercial; p < 0.008 and 0.001) were observed, with the odds ratios of the commercial farm having Stronglyes spp. and Eimeria spp. of 1.3 (CI = 0.6–2.9) and 4.8 (CI = 2.5–9.1). Mortalities from endoparasitism were only recorded at the commercial farm, with the loss of 24 goats in the final 3 months of the dry season (Feb-April). This study identified a moderate prevalence of multiple endoparasitic species in smallholder goat farms that appeared well-tolerated, whereas in the developing commercial system, endoparasites posed significant risks to enterprise viability, even with use of anthelmintics. Further studies on endoparasite control are required if commercial tropical goat meat production is to prove sustainable and assist in addressing regional food security, plus provide a pathway to improve the livelihoods of Lao goat smallholders seeking to expand and intensify their enterprises.