I propose three solutions, with the rotated titles on two centred lines. I load tabularx,makecellto improve padding of cells and allow line breaks in cells,booktabs` in two solutions:
\documentclass[12pt]{article}
\usepackage{geometry} \usepackage{mathtools,amssymb}
\usepackage[dvipsnames]{xcolor}
\usepackage[geometry]{ifsym}
\usepackage{multirow, tabularx, makecell, rotating, graphicx, siunitx, booktabs}
\newcommand\rottitle[2]{\multirowcell{#1}{\rotatebox[origin =r]{90}{\begin{tabular}{@{}c@{}}#2\end{tabular}}}}%
\begin{document}
\begin {table}%
\centering\sisetup{table-format=1.2, table-number-alignment=center}
\setcellgapes{4pt}\makegapedcells
\begin{tabularx}{0.8\linewidth}{|c|X|*{3}{S|}}
\hline
& & {\makecell{Objem z DVH & & \\{} [\si{cm³}]}} & {\makecell{a \\{} [cm]}} & {\makecell{$V_{\text{exp}}$ \\{}[\si{cm³}]}}\\
\hline
\rottitle{2}{CT1 & & & & \\ 1\,mm} & Medzi $10$ a $9,5 Gy$ & 7,82 & 0,97 & 8,73 \\
& Medzi $10,5$ a $10 Gy$ & 8,3 & 0,91 & 8,19 \\
\hline
\rottitle{2}{CT1\\ 3\,mm}%
& Medzi $10$ a $9,5 Gy$ & 7,31 & 1 & 9 \\
& Medzi $10,5$ a $10 Gy$ & 8,43 & 0,98 & 8,82 \\
\hline
\rottitle{2}{CT2 & & & & \\ 1\,mm} & Medzi $10$ a $9,5 Gy$ & 8,02 & 1,01 & 9,09 \\
& Medzi $10,5$ a $10 Gy$ & 8,73 & 0,97 & 8,73 \\
\hline
\rottitle{2}{CT2 & & & & \\ 3\,mm }& Medzi $10$ a $9,5 Gy$ & 7,57 & 0,96 & 8,64 \\
& Medzi $10,5$ a $10 Gy$ & 7,91 & 0,91 & 8,19 \\
\hline
\hline
\end{tabularx}
\caption{table}
\label{table}
\end {table}
\begin {table}% [H]
\centering\sisetup{table-format=1.2, table-number-alignment=center}
\setcellgapes{3pt}\makegapedcells
\begin{tabularx}{0.8\linewidth}{cX*{3}{S}}
& & {\makecell{Objem z DVH & & \\{} [\si{cm³}]}} & {\makecell{a \\{} [cm]}} & {\makecell{$V_{\text{exp}}$\\{} [\si{cm³}]}}\\
\toprule
\rottitle{2}{CT1 & & & & \\ 1\,mm} & Medzi $10$ a $9,5 Gy$ & 7,82 & 0,97 & 8,73 \\
& Medzi $10,5$ a $10 Gy$ & 8,3 & 0,91 & 8,19 \\
\addlinespace
\rottitle{2}{CT1\\ 3\,mm}%
& Medzi $10$ a $9,5 Gy$ & 7,31 & 1 & 9 \\
& Medzi $10,5$ a $10 Gy$ & 8,43 & 0,98 & 8,82 \\
\cmidrule(lr){1-5}
\rottitle{2}{CT2 & & & & \\ 1\,mm} & Medzi $10$ a $9,5 Gy$ & 8,02 & 1,01 & 9,09 \\
& Medzi $10,5$ a $10 Gy$ & 8,73 & 0,97 & 8,73 \\
\addlinespace
\rottitle{2}{CT2 & & & & \\ 3\,mm }& Medzi $10$ a $9,5 Gy$ & 7,57 & 0,96 & 8,64 \\
& Medzi $10,5$ a $10 Gy$ & 7,91 & 0,91 & 8,19 \\
\bottomrule
\end{tabularx}
\caption{table}
\label{table}
\end {table}
\begin {table}% [H]
\centering\sisetup{table-format=1.2, table-number-alignment=center}
\setcellgapes{3pt}\makegapedcells
\begin{tabularx}{0.8\linewidth}{cX*{3}{S}}
& & {\makecell{Objem z DVH & & \\{} [\si{cm³}]}} & {\makecell{a \\{} [cm]}} & {\makecell{$V_{\text{exp}}$\\{} [\si{cm³}]}}\\
\cmidrule[\heavyrulewidth]{2-5}
\rottitle{2}{CT1 & & & & \\ 1\,mm} & Medzi $10$ a $9,5 Gy$ & 7,82 & 0,97 & 8,73 \\
& Medzi $10,5$ a $10 Gy$ & 8,3 & 0,91 & 8,19 \\
\cmidrule(lr){2-5}
\rottitle{2}{CT1\\ 3\,mm}%
& Medzi $10$ a $9,5 Gy$ & 7,31 & 1 & 9 \\
& Medzi $10,5$ a $10 Gy$ & 8,43 & 0,98 & 8,82 \\
\cmidrule(lr){2-5}
\morecmidrules
\cmidrule(lr){2-5}
\rottitle{2}{CT2 & & & & \\ 1\,mm} & Medzi $10$ a $9,5 Gy$ & 8,02 & 1,01 & 9,09 \\
& Medzi $10,5$ a $10 Gy$ & 8,73 & 0,97 & 8,73 \\
\cmidrule(lr){2-5}
\rottitle{2}{CT2 & & & & \\ 3\,mm }& Medzi $10$ a $9,5 Gy$ & 7,57 & 0,96 & 8,64 \\
& Medzi $10,5$ a $10 Gy$ & 7,91 & 0,91 & 8,19 \\
\cmidrule[\heavyrulewidth]{2-5}
\end{tabularx}
\caption{table}
\label{table}
\end {table}
\end{document}

P{...}. – Zarko May 04 '16 at 19:35