In recent years the demand for domestic goat and sheep milk cheeses has been increasing. Typically, these cheeses are artisanal or semi-artisanal in nature and targeted towards value-added niche markets. Strong market demand has created new opportunities for artisanal cheesemaking but has also created pressure to expand scale of production. At the farmstead scale of production, artisanal cheesemakers often lack well-defined schedules for optimum acidity during manufacture and well defined parameters for finished product composition (e.g., moisture, fat, salt, pH). As scale of production increases, the need to monitor and optimize acidity schedule and finished product composition to assure quality and safety becomes more acute. Thus, the development of analytical monitoring systems tailored to artisanal cheeses is an important technical hurdle that must be addressed as the industry grows. Integrating this analytical data into the artisanal practices of the cheesemaker and affineur, thereby combining the art of cheesemaking with the science of cheesemaking, is a further challenge. At larger scales of production, accurate prediction of the cheese yielding capacity of the milk to facilitate inventory control and pricing for producer payment becomes essential. To this end, a better understanding of the factors that influence the cheese yielding potential of sheep and goat milk (e.g., seasonal changes in milk composition, SCC, casein number) is needed to develop valid yield equations. Thus, the future growth of goat and sheep milk cheesemaking in the U.S. will depend in part on whether artisanal practices can be augmented with science-based management tools to enable better control of starter performance, product composition, milk quality and cheese yield. Such tools are well developed for the cow milk cheese industry but will need to be tailored for sheep and goat milk cheeses. Beyond this, future success of this industry will depend upon continued access to value-added niche markets. Such access may be jeopardized if pasteurization of cheesemilk becomes mandatory for all cheeses because much of this industry is oriented towards upscale, highly value-added raw milk cheese niche markets. Therefore, there is an urgent need for research aimed at developing practical alternatives to pasteurization, such as farmstead HACCP-type systems, that can reduce the level of risk associated with raw milk cheeses to that of pasteurized milk cheeses. Such research should solicit the participation of regulatory authorities and industry groups at the earliest stages to target strategies that are both practical to implement and capable of reducing risk to levels sufficient to satisfy regulatory concerns.