CREATE TABLE `article` (
  `articleID` int(11) NOT NULL AUTO_INCREMENT,
  `reference` varchar(255) DEFAULT NULL,
  `addDt` datetime DEFAULT NULL,
  PRIMARY KEY (`articleID`)
) ENGINE=InnoDB AUTO_INCREMENT=1 DEFAULT CHARSET=utf8;


CREATE TABLE `articleRelated` (
  `articleID` int(11) NOT NULL,
  `relatedArticleID` int(11) NOT NULL,
  PRIMARY KEY (`articleID`,`relatedArticleID`),
  KEY `a1` (`articleID`),
  KEY `a2` (`relatedArticleID`),
  CONSTRAINT `a1` FOREIGN KEY (`articleID`) REFERENCES `article` (`articleID`) ON DELETE NO ACTION ON UPDATE NO ACTION,
  CONSTRAINT `a2` FOREIGN KEY (`relatedArticleID`) REFERENCES `article` (`articleID`) ON DELETE NO ACTION ON UPDATE NO ACTION
) ENGINE=InnoDB DEFAULT CHARSET=utf8;

<?php
/**
 * Model for article
 * 
 * @Table(name="article") 
 * @Entity
 */
class App_Model_Article
{

    /**
     * @var integer articleID
     * @Column(name="articleID", type="integer", nullable=false) 
     * @GeneratedValue(strategy="IDENTITY") 
     * @Id
     */
    protected $_articleID = null;

    /**
     * @var string reference
     * @Column(name="reference", type="string", nullable=true, length=255)
     */
    protected $_reference = null;

    /**
     * @var datetime addDt
     * @Column(name="addDt", type="datetime", nullable=true)
     */
    protected $_addDt = null;

    /**
     * @OneToMany(targetEntity="App_Model_ArticleRelated", mappedBy="_article", cascade={"persist"})
     */
    protected $_articleRelatedRefArticle = array();

    /**
     * @OneToMany(targetEntity="App_Model_ArticleRelated", mappedBy="_relatedArticle", cascade={"persist"})
     */
    protected $_articleRelatedRefRelatedArticle = array();
}

<?php

/**
 * Model for articleRelated
 * 
 * @Table(name="articleRelated") 
 * @Entity
 */
class App_Model_ArticleRelated
{

    /**
     * @ManyToOne(targetEntity="App_Model_Article") 
     * @JoinColumn(name="articleID", referencedColumnName="articleID") 
     * @Id
     */
    protected $_article = null;

    /**
     * @ManyToOne(targetEntity="App_Model_Article") 
     * @JoinColumn(name="relatedArticleID", referencedColumnName="articleID") 
     * @Id
     */
    protected $_relatedArticle = null;
}

$firstArticle = $this->_entityManager->find('App_Model_Article', 54);
      
$related = $firstArticle->getArticleRelated('article');
foreach ($related as $art) {
       	var_dump($art);
}

SELECT , t1.articleID AS articleID0, t1.relatedArticleID AS relatedArticleID2 FROM articleRelated t1 WHERE articleID = ?

//...
protected function _getSelectColumnListSQL()
    {
        if ($this->_selectColumnListSql !== null) {
            return $this->_selectColumnListSql;
        }

        $columnList = '';

        // Add regular columns to select list
        foreach ($this->_class->fieldNames as $field) {
            if ($columnList) $columnList .= ', ';
            $columnList .= $this->_getSelectColumnSQL($field, $this->_class);
        }

        $this->_selectColumnListSql = $columnList . $this->_getSelectJoinColumnsSQL($this->_class);
		
        return $this->_selectColumnListSql;
    }
//....

$this->_selectColumnListSql = trim($columnList . $this->_getSelectJoinColumnsSQL($this->_class), ',');