Direct and indirect sources of CO₂, CH₄, and N₂O emissions in animal production systems includes the animals, feed storage areas, manure deposition and storage areas, and feed and forage production fields. These 3 gases comprise the primary greenhouse gas (GHG) emissions from animal feeding operations. Each GHG may be more or less prominent from each emitting source. Similarly, species dictates importance of enteric CH₄ emissions. Measures of GHG flux from animals are often made using respiration chambers for measurement of concentration and flux, head boxes or halters allowing for measures of concentration directly and flux indirectly (tracer gas techniques), or in vitro gas production techniques. Concentration measures are made using gas chromatography, photoacoustic, open path Fourier transform infrared (FTIR) or non-dispersive infrared (NDIR) spectroscopy. The prominent methods for measuring GHG emissions from housing include tracer gas techniques (indirect ventilation measures) or direct ventilation measures, each coupled with concentration measures of gases of interest. Methods for collecting and measuring GHG emissions from manure storage and/or production lots include use of downwind concentration measures combined with modeling techniques, static chambers or flux hood methods. Similar methods can be deployed for determining GHG emissions from fields. Each method identified has its own benefits and challenges to use for the stated application. Considerations for use include intended goal, compatibility with production system, equipment investment and maintenance, frequency and duration of sampling needed to achieve desired representativeness of emissions over time, accuracy and precision of the method, and environmental influences on the method. In the absence of a perfect method for all situations, full knowledge of the advantages and disadvantages of each method is extremely important during the development of the experimental design and interpretation of results. Attributes of the various options for measuring GHG flux from different sources within a farming system will be discussed including methods to measure both concentration of gas and flux from the various emission sources.