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Orange roughy form dense spawning aggregations in specific small areas in deep water on the Namibian shelf between late June and early August each year. The biomass in three such areas, where most commercial fishing occurs (the Johnies, Frankies and Rix Quota Management Areas, or QMAs) has been assessed acoustically each year since 1997. Acoustic estimates of the aggregated portion of the biomass (the only component that can be assessed reliably using acoustics) were obtained for all three QMAs in 1997 and 1998, but only for Frankies in 1999 owing to increased problems with target identification as the biomass declined. The methodology developed for these surveys, including the equipment used, survey design, target identification, data processing and error analysis are described. Some important biases that should be corrected for when estimating absolute abundance of orange roughy acoustically are addressed. Individual sources of error were quantified as well as possible, and input to an error model that simulated the error process and produced probability density functions of absolute biomass, from which the mean absolute biomass and its standard error could be computed for each survey, effectively correcting for identified sources of bias and quantifying the overall uncertainty. The correction factors ranged from 1.58 to 1.71 and the CVs increased by factors of 1.2–2.1. Target strength uncertainty and negative bias attributable to the dead zone close to the bottom were considered to be the most serious errors. The acoustic estimates indicate a substantial decline in orange roughy biomass in all three QMAs since 1997, in accord with indices from contemporaneous swept-area surveys and the catch rate of the commercial fleet. Acoustic estimates have already been used extensively to manage the resource and are likely to remain important in the future.