Use prepared statements and parameterized queries. These are SQL statements that are sent to and parsed by the database server separately from any parameters. This way it is impossible for an attacker to inject malicious SQL.

You basically have two options to achieve this:
1. Using PDO (for any supported database driver):

$stmt = $pdo->prepare('SELECT * FROM employees WHERE name = :name');

$stmt->execute(array('name' => $name));

foreach ($stmt as $row) {
    // do something with $row
}

2. Using MySQLi (for MySQL):

$stmt = $dbConnection->prepare('SELECT * FROM employees WHERE name = ?');
$stmt->bind_param('s', $name); // 's' specifies the variable type => 'string'

$stmt->execute();

$result = $stmt->get_result();
while ($row = $result->fetch_assoc()) {
    // do something with $row
}

Correctly setting up the connection

Note that when using PDO to access a MySQL database real prepared statements are not used by default. To fix this you have to disable the emulation of prepared statements. An example of creating a connection using PDO is:

$dbConnection = new PDO('mysql:dbname=dbtest;host=127.0.0.1;charset=utf8', 'user', 'pass');
$dbConnection->setAttribute(PDO::ATTR_EMULATE_PREPARES, false);
$dbConnection->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
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