Acetylcholinesterase (AChE) is a significant component of the membrane contributing to the permeability changes during synaptic transmission and conduction. Phenylketonuria is a group of metabolic disorders in which phenylalanine (Phe) is highly elevated in blood (up to 0.1 M) resulting in mental retardation etc. AChE activity was measured spectrophotometrically after incubation with various Phe concentrations. Phe interaction with DNA was evaluated with an established HPLC method. Phe was found to inhibit AChE almost 40%, at a concentration of 5 mM, whereas a 62.5% DNA peak exclusion (molecular interaction) was observed when Phe was incubated with DNA at a concentration of 3 mM. In addition the ratio of DNA: Phe determined the potency of the observed molecular effect.