Archaeal membranes are composed of core lipids called glycerol dialkyl glycerol tetraethers (GDGTs) that contain polar head groups (intact GDGTs) in living cells. The reliability of Archaeal membrane lipids in studies of paleogeochemistry, population distributions, and physiological state depend on efficient extraction and detection of these lipids. We compare existing methods for extraction of core and intact GDGTs so that they can be used as quantitative indicators of living archaeal biomass. We used an active culture of the marine archaeon, Nitrosopumilus maritimus, to document limitations of methods in current use and as a reference for methodological improvement. We found that all extractable GDGTs in the culture were intact and that acid hydrolysis is the only way to quantitatively recover GDGTs from exponentially growing cells. Because acid hydrolysis removes polar head groups, it is not suitable for analysis of intact lipids. In contrast to the culture, high recovery was achieved for intact and core lipids from environmental samples, including water column particles, sediments, and soils. The high recovery from environmental samples and the large portion of core GDGTs relative to intact GDGTs suggest that lipids in the environment are largely derived from dead or dying cells. Because previous studies measured core GDGTs without acid hydrolysis, lipids contained in living cells were not detected and thus these results do not reflect viable biomass. We present a method to accurately quantify living and relict GDGTs by choosing the most efficient extraction protocol and measuring core GDGTs in extracts before and after acid hydrolysis. Here we set out to develop a method to use I-GDGTs as quantitative tracers of viable cell abundance in the environment Sturt et al. 2004). Using traditional extraction techniques on cultures of the mesophilic marine crenarchaeota, Nitrosopumilus maritimus, we discovered that lipid yields per cell varied considerably depending on the extraction technique used. Whereas it is well known that membrane lipids of archaeal cells can be difficult to extract, there are no recent reports that quantify the efficiency of currently used extraction techniques. Moreover, researchers often give no rationale for choosing one extraction protocol over another. As applications of both core and intact GDGTs grow, it is important to compare and unify GDGT extraction techniques. We searched the literature for GDGT extraction methods and measured the efficiency and degree of polar head group loss for each method using a culture of exponentially growing N. maritimus that contained only I-GDGTs. We then analyzed samples from environments where GDGT-based proxies are commonly measured, including marine water column particles, marine sediments, and soils.We evaluated five basic techniques: solvent extraction with mild acid to enhance the lyses of archaeal cells (e.g., Bligh and Dyer 1959;Nishihara and Koga 1987), accelerated solvent extraction (ASE) (e.g., Huguet et al. 2007b; Kim et al. 2008), ...