Over 70% of the population of Afghanistan is considered rural and largely dependent on livestock for their lives and livelihoods, particularly small ruminants (sheep and goats). Despite the presence of conflict and invasion since the 1970s, the country has developed a veterinary infrastructure to provide a mechanism for disease reporting and laboratory confirmation of disease presence. Records from the central veterinary diagnostic laboratory’s information management system from 2015-2017 were analyzed to establish the status of reporting and testing procedures in sheep and goats. Of 1706 records for sheep and 962 for goats, 565 and 237 had positive findings of disease, respectively. Records with positive findings underwent case-by-case review to identify specific laboratory confirmed diseases and extract checklists of clinical signs observed in the field and suspect diseases recorded prior to laboratory submission. Presence of intestinal parasites was the most common laboratory diagnosis in sheep, followed by Peste des Petits Ruminants (PPR), Clostridium perfringens, and sheep & goat pox; among goats, the most commonly diagnosed were PPR, sheep & goat pox, and Mycoplasma species. In 79% of sheep and 84% of goats, no clinical signs were entered, and suspect diagnoses were entered for 44% of sheep and 78% of goats. Small sample sizes and painstaking, time-consuming, case-by-case review needed to process records for analysis were limiting factors in the current report. Making improvements at each step of the laboratory documentation system will help ensure that useful summary output is readily available for monitoring and evaluating purposes in the future.