In classical thermodynamics the change in internal energy is defined by the first law as
$$\Delta U = q + w$$
so that only the difference in $U$ is known; $q$ is the heat absorbed by the 'system' and $w$ the work done on the system.
For example in a closed system (no exchange of matter with environment) we can write for a reversible change
\begin{align}
\mathrm{d}q &= T\mathrm{d}S \\
\mathrm{d}w &= -p\mathrm{d}V
\end{align}
and then if the only form of work on a gas is volume change
$$ \mathrm{d}U = T\mathrm{d}S - p\mathrm{d}V$$
and this is the fundamental equation for a closed system. Thus only difference in internal energy are measurable from thermodynamics, and this follows from the first law. (Even if you integrate this equation from say state $a$ to $b$ the result will be $U(b)-U(a)=\ddot {}$ in other words $\Delta U$.)
Thermodynamics was developed before the nature of matter was known, i.e. it does not depends on matter being formed of atoms and molecules. However, if we use additional knowledge about the nature of molecules then the internal energy (and entropy) can be determined from statistical mechanics.
The internal energy ($U$ not $\Delta U$) of a perfect monoatomic gas is the ensemble average and is
$$U=(3/2)NkT$$
or in general $U=(N/Z)\Sigma_ j\exp(−\epsilon_j/(kT))$ where $Z$ is the partition function, $k$ Boltzmann constant, $\epsilon_j$ energy of level $j$, and $T$ temperature and $N$ Avogadro's number. The absolute value of the entropy $S$ (for a perfect monoatomic gas) can also be determined and is given by the Sakur-Tetrode equation.