A participatory epidemiological (PE) study was conducted with livestock keepers in Moroto and Kotidodistricts, Karamoja Region, Uganda, between October and December 2013 to determine the management options and relative importance of tick-borne diseases (TBDs) amongst transhumant zebu cattle. Data collection involved 24 focus group discussions (each comprising 8–12 people) in 24 settlement areas (manyattas), key informant interviews (30), direct observation, a review of surveillance data, clinical examination, and laboratory confirmation of cases of TBDs. Methods used in group discussions includedsemi-structured interviews, simple ranking, pairwise ranking, matrix scoring, proportional piling andparticipatory mapping. The results of pairwise comparison showed the Ngakarimojong-named diseases, lokit (East Coast fever, ECF), lopid (anaplasmosis), loukoi (contagious bovine pleuropneumonia, CBPP), lokou (heartwater) and lokulam (babesiosis), were considered the most important cattle diseases in Moroto in that order, while ECF, anaplasmosis, trypanosomosis (ediit), CBPP and nonspecific diarrhoea (loleo) were most important in Kotido. Strong agreement between informant groups (Kendall’s coeffi-cient of concordance W = 0.568 and 0.682; p < 0.001) in pairwise ranking indicated that the diseases werea common problem in selected districts. East Coast fever had the highest median score for incidence (18%[range: 2, 33]) in Moroto, followed by anaplasmosis (17.5% [8,32]) and CBPP (9% [1,21]). Most animalsthat suffered from ECF, anaplasmosis, heartwater and babesiosis died, as the respective median scoresfor case fatality rates (CFR) were 89.5% (42, 100), 82.8% (63, 100), 66.7% (20, 100) and 85.7% (0, 100).In Kotido, diseases with high incidence scores were ECF (21% [6,32]), anaplasmosis (17% [10,33]) andtrypanosomosis (8% [2,18]). The CFRs for ECF and anaplasmosis were 81.7% (44, 100) and 70.7% (48, 100),respectively. Matrix scoring revealed that disease indicators showed strong agreement (W = 0.382–0.659,p < 0.05–p < 0.001) between informant groups. Inadequate knowledge, poor veterinary services and lim-ited availability of drugs were the main constraints that hindered the control of TBDs. Hand picking ofticks was done by all pastoralists while hand spraying with acaricides was irregular, often determined byavailability of drug supplies and money. It was concluded that TBDs, particularly ECF and anaplasmosiswere important diseases in this pastoral region. Results from this study may assist in the design of feasible control strategies.