Alkaline Phosphatase (ALP) enzyme activity is usually measured as a part of liver function test (LFT) to detect increases in its activity. Less attention has been put to know the conditions associated with decreases in its activity. Micronutrients like Zinc (Zn) and Magnesium (Mg) are important causes of low ALP activity. Our Objective is to find out Zn and Mg deficiencies as important cause of decrease in ALP activity and to initiate supplementation of these minerals. The study was done to assess Zn and Mg deficiency in 42 persons having low ALP activity and 45 healthy controls. Correlation between minerals and ALP activities were also carried out. It was found that 52.38% of cases are Mg deficient and 47.62% cases are Zn deficient. A significant decrease in Zn and Mg was observed in low ALP cases when compared with control (p<0.001, p<0.05). Significant positive correlation was found between the minerals and ALP. Serum Zn and Mg are essential for human body and by screening their deficiency, supplementation of minerals can be initiated.