The molecular mass (m) is the mass of a given molecule: it is measured in daltons or atomic mass (Da or u). Different molecules of the same compound may have different molecular masses because they contain different isotopes of an element. The related quantity relative molecular mass, as defined by IUPAC, is the ratio of the mass of a molecule to the unified atomic mass unit (also known as the dalton) and is unitless. The molecular mass and relative molecular mass are distinct from but related to the molar mass. The molar mass is defined as the mass of a given substance divided by the amount of a substance and is expressed in g/mol. That makes the molar mass an average of many particles or molecules, and the molecular mass the mass of one specific particle or molecule. The molar mass is usually the more appropriate figure when dealing with macroscopic (weigh-able) quantities of a substance.

The definition of molecular weight is most authoritatively synonymous with relative molecular mass; however, in common practice, it is highly variable. When the molecular weight is used with the units Da or u, it is frequently as a weighted average similar to the molar mass but with different units. In molecular biology, the mass of macromolecules is referred to as their molecular weight and is expressed in kDa, although the numerical value is often approximate and representative of an average.

The terms molecular mass, molecular weight, and molar mass are often used interchangeably in areas of science where distinguishing between them is unhelpful. In other areas of science, the distinction is crucial. The molecular mass is more commonly used when referring to the mass of a single or specific well-defined molecule and less commonly than molecular weight when referring to a weighted average of a sample. Prior to the 2019 redefinition of SI base units quantities expressed in daltons (Da or u) were by definition numerically equivalent to otherwise identical quantities expressed in the units g/mol and were thus strictly numerically interchangeable. After the 20 May 2019 redefinition of units, this relationship is only nearly equivalent.

The molecular mass of small to medium size molecules, measured by mass spectrometry, can be used to determine the composition of elements in the molecule. The molecular masses of macromolecules, such as proteins, can also be determined by mass spectrometry; however, methods based on viscosity and light-scattering are also used to determine molecular mass when crystallographic or mass spectrometric data are not available.