Magnesium (Mg) is an essential divalent cation involved in various enzymatic reactions that regulate vital biological functions. The main goal was to evaluate Mg status and its association with nutritional indicators in 78 children and adolescents with chronic diseases. We assessed anthropometric, biochemical, diet, body composition, and bone densitometry valuations. Serum Mg and Ca levels were determined using the standardized method and diet calcium (Ca) and Mg consumption by a prospective 72 h diet survey. Mean serum Ca (9.9 mg/dL), Mg (2.08 mg/dL) dietary Ca (102% DRI: Dietary Reference Intake), and Mg intake (105% DRI) were normal. A total of 45% had hypomagnesemia, 12% had hypermagnesemia, and 26% and 24% had inadequate and high Mg intake, respectively. Only 6% of patients had poor Mg intake and hypomagnesemia, and 54% and 90% of our series had an elevated serum Ca/Mg ratio > 4.70 (mean 4.79) and a low Ca/Mg intake ratio < 1.70 (mean 1.06), respectively. Both Ca/Mg ratios were linked with the risk of developing other chronic conditions such as cardiovascular disease, type 2 diabetes, syndrome metabolic, and even several cancers. Therefore, 79% of children and adolescents with chronic diseases were at elevated risk of having abnormal Mg status and developing other chronic illnesses.