In 2012, United Nations Office on Drugs and Crime (UNODC) estimated that, in 2010, between 3.4 and 6.6% of the world’s population, aged between 15 and 64 years, had used an illicit substance at least once in the previous year; moreover, almost 12% of illicit drug users reported some kind of problems, including drug dependence and drug-use disorders. Among the main illicit drugs, global statistics showed that 0.3–0.4% of the population aged between 15 and 64 years use cocaine (COC) (1). In Brazil, an increase in COC and tobacco consumption has been noted; according to the Brazilian Center of Information on Psychotropic Drugs (CEBRID), in 2005, the prevalence of the use of COC and crack in the 108 largest cities in Brazil was 2.9 and 0.7%, respectively. Recent statistics on the extent of use of illicit drugs given by the UNODC (2012) report that this consumption by Brazilian women is approximately one-third of the use among men, whereas in other countries the rate is one-tenth (1, 2). Current data indicate an increase in drug use by women of reproductive age. A study by the Ministry of Health of Sa˜ o Paulo showed an increase in 91% of hospital admissions of women in the last 3 years due to COC use. According to a research in the Hospital Faculty of Medicine of Ribeira˜ o Preto, that used interviews and toxicological analyses, it was found that the incidence of COC use in mothers was 6% and tobacco use was 31% during pregnancy (3). In addition to illicit drugs, licit drugs represent a danger to human health. Tobacco has become a public health concern due to the risks associated with smoking and environmental exposure to tobacco smoke. Today, more than one billion people are smokers worldwide (1). In 2008, the Brazilian Institute of Geography and Statistics (IBGE) reported that 17.2% of the Brazilian population aged over 15 years regularly used tobacco (4). The prevalence of COC and tobacco use by pregnant women has become a major public health issue. In 2011, the National Survey on Drug Use and Health (NSDUH), in the USA, reported that 5.0% of the pregnant women aged 15–44 years were current illicit drug users; 17.6% of these women had smoked cigarettes in the previous month (5). Exposure of pregnant women to drugs has serious consequences on the health of the fetus, which manifest themselves before and after birth. COC crosses the placenta without undergoing metabolism with direct action on the fetal vasculature causing vasoconstriction and urogenital, cardiovascular and central nervous system malformations (6). Tobacco use by the mother decreases the fetal growth rate, because it increases the level of carboxyhemoglobin in fetal blood. Moreover, the exposure to tobacco may induce abortion, placental abruption and sudden infant death syndrome during and after pregnancy (7). In utero drug exposure can be evaluated soon after birth by investigating analytes and metabolites in meconium samples. The assessment of this exposure is crucial to identify, treat and monitor newborns displaying symptoms typical of drug withdrawal. A qualitative or quantitative analysis of drugs, metabolites and biomarkers can be conducted in several types of biological matrices (conventional matrices), such as plasma, serum, whole blood, saliva, urine and tissues (8). Recently, studies have used alternative biological samples, such nails, hair, umbilical cord, amniotic fluid and meconium (9–11). Meconium, the first fecal matter passed by a neonate, begins to form at 12 weeks of gestation, which makes the specimen the biological matrix of choice for detecting in utero drug exposure. It is a heterogeneous and complex sample consisting of water, desquamated epithelial cells of the gastrointestinal tract and skin and various substances such as acids and bile salts, cholesterol, enzymes, sugars, proteins, pancreatic and intestina .....