Colony Collapse Disorder is the term used to describe the recent decline in honey bee populations in the United States. This decline has been attributed to several variables; including viruses, parasites, poor nutrition, and exposure to neonicotinoid insecticides. Liquid chromatography with tandem mass spectrometry detection is the technique of choice for analysis of neonicotinoids. Over the past 5 years, studies have been initiated to determine the level of exposure of honey bees to neonicotinoids. These pollinator health studies involve the collection and analysis of pollen and nectar from target agricultural crops to determine the magnitude of residues. Common to these sample matrices are the extremely small sample sizes. Pollen and nectar samples collected from plants are commonly less than 100 mg in mass, and the entire field sample is typically extracted. Study requirements for limit of quantitation and detection are also very low (<1 ppb). Small sample size and low LOQ/LOD requirements present challenges in the analytical laboratory. However, these matrices lend themselves well to the application of high-throughput sample preparation techniques. This research provides bridging data for a representative neonicotinoid insecticide, thiamethoxam, and its major metabolite clothianidin . The use of a bead mill extraction apparatus and 96 well plate solid-phase extraction demonstrated acceptable accuracy and precision, and results were comparable to conventional extraction and cleanup techniques. Fortification recovery using high-throughput techniques at the LOQ and 10x LOQ levels were in excess of 80% with a relative standard deviation of <20%. Utilization of these techniques will help laboratories meet the throughput requirements for the ever increasing number of pollinator health studies to be conducted in the near future.