Disclosed herein are methods for diagnosing carnitine deficiency in patients and quantifying that deficiency such that carnitine concentrations can be easily and accurately tracked within a given patient over time. Particular embodiments disclosed herein pertain to methods for diagnosing and quantifying the level of carnitine deficiency in patients undergoing dialysis procedures. The diagnosing and quantifying methods allow high throughput and low cost handling while providing high sensitivity and accuracy analysis such that the methods can be used frequently to monitor patient status, diagnose carnitine deficiency, and manage appropriate therapies to treat carnitine deficiency. The preferred embodiments disclosed herein utilize plasma samples taken from patients and dried on filter paper, which samples are then later analyzed using electrospray tandem mass-spectrometry and quantified in a manner that accounts for various complications that can skew free carnitine, acylcarnitine, or total carnitine concentrations.