The endocannabinoids anandamide and 2-arachidonoylglycerol, as well as several anandamiderelated N-acylethanolamines, belong to a family of lipid transmitter regulating fundamental physiological processes, including neurotransmission and neuroinflammation. Their precise quantification in biological matrices can be achieved by gas chromatography/mass spectrometry (GC-MS), but this method typically requires multiple time-consuming purification steps, such as solid-phase extraction followed by HPLC. Here we report a novel solid-phase extraction procedure allowing for single-step and thus higher-throughput purification of endocannabinoids and Nacylethanolamines before GC-MS quantification. We determined the minimal amount of mouse brain tissue required to reliably detect endocannabinoids and N-acylethanolamines when using this approach and provide direct evidence for quantification accuracy by using radioactive and deuterated standards spiked into mouse brain samples. Using this approach we found that mouse brain contains much higher levels of anandamide (> 1 nmol/g of tissue) than previously reported, whereas levels of 2-arachidonoylglycerol and other N-acylethanolamines are well-within the range of previous reports. In addition we show that mouse brain amounts of endocannabinoids and Nacylethanolamines differ depending on animal gender, as well as on whether the tissue was fixed or not. Our study shows that endocannabinoids and N-acylethanolamines levels quantified in mouse brain by GC-MS closely depend on tissue amount and preparation, as well as on animal gender, and that depending on such parameters, anandamide levels could be underestimated.